Watson-Crick base pairings

Fig. 8. Non-Watson-Crick base pairs occurring in double-stranded RNA where — represents the site of attachment to the sugar (a) A—U reverse-Watson-Crick (b) G—C reverse-Watson-Crick (c) A—U Hoogsteen (d) A—U reverse-Hoogsteen (e) G—U wobble and (f) G—U reverse-wobble.

Structural Equivalence of Watson-Crick Base Pairs... 

Owing to the increasing efficiency of computational methods, it has become possible to investigate base pairs in the gas phase and solution simulated by super-molecular approaches with up to six water molecules [98IJQ37, 98JPC(A) 10374, 98JPC(B)9109, 99JST107]. In the cytosine-isocytosine Watson-Crick base pair. 

ASON are sequences of usually 17-30 bases of single-stranded DNA that hybridize to specific genes or their mRNA products by Watson-Crick base pairing and disrupt their function. In the case of AS-ODN (antisense oligodeoxyribonucleotides) cellular RNAseH is able to bind to the DNA-RNA duplex and hydrolyze the RNA, resulting in increased transcript turnover. Modifications to the deoxy moiety at the 2 -sugar position prohibits RNAse H action. 

This is consistent with there not being enough space (20 °) for two purines to fit within the helix and too much space for two pyrimidines to get close enough to each other to form hydrogen bonds between them. These relationships are often called the rules of Watson-Crick base pairing. 

Fig. 3.2 Pairing rules for polyamide recognition of all four Watson—Crick base pairs of DNA. Putative hydrogen bonds are shown as dashed lines. Circles with dots represent lone pairs of N(3) of purines and 0(2) of pyrimi-...

White, S., J.W. Szewczyk, J.M. Turner, E.E. Baird, and P.B. Dervan. Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands. Nature 1998, 393, 468-471. 

Fig. 4.3 Triplex invasion by homopyrimidine PNA oligomers. One PNA strand binds via Watson-Crick base pairing (preferably in the antiparallel orientation), while the other binds via Hoogsteen base pairing (preferably in the parallel orientation). It is usually advanta-...

The fundamental a-hehcal peptide nucleic acid (aPNA) concept is illustrated in Fig. 5.2. Our prototype aPNA module incorporated five nucleobases for Watson-Crick base pairing with a single-stranded nucleic acid target. These nucleobases... 

The amino acid sequence of our first aPNA (which we termed backbone 1 or bl) was designed based on this amphipathic hehx sequence (Fig. 5.3 B). Specifically, this aPNA backbone included hydrophobic amino acids (Ala and Aib), internal salt bridges (Glu-(aa)3-Lys-(aa)3-Glu), a macrodipole (Asp-(aa)i5-Lys), and an N-ace-tyl cap to favor a-helix formation. The C-termini of these aPNA modules end in a carboxamide function to preclude any potential intramolecular end effects. Each aPNA module incorporates five nucleobases for Watson-Crick base pairing to a target nucleic acid sequence. 

Lee et al. [60] investigated the adhesion of a single pair of DNA strands. They identified two types of forces interchain forces associated with Watson-Crick base pairing between complementary strands, and intrachain forces associated with the elasticity of single strands. For studying interchain interactions, complementary oligomers (ACTG)s and... 

The DNA double heUx illustrates the contribution of multiple forces to the structure of biomolecules. While each individual DNA strand is held together by covalent bonds, the two strands of the helix are held together exclusively by noncovalent interactions. These noncovalent interactions include hydrogen bonds between nucleotide bases (Watson-Crick base pairing) and van der Waals interactions between the stacked purine and pyrimidine bases. The hehx presents the charged phosphate groups and polar ribose sugars of... 

The processes of DNA and RNA synthesis are similar in that they involve (1) the general steps of initiation, elongation, and termination with y to 3 polarity (2) large, multicomponent initiation complexes and (3) adherence to Watson-Crick base-pairing rules. These processes differ in several important ways, including the... 

Fig. 33. Watson-Crick base pairs [C-G], [C-G-lVZmetai]. [C-NimetflrG]. Adapted from Ref. (117).

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